v6717

New parameters to add No new parameters

SVN commit message

r6717 | ful083 | 2024-06-24 17:43:19 -0700 (Mon, 24 Jun 2024) | 1 line Changed paths: M /Atlantis/trunk/atlantis/atecology/atmigration.c M /Atlantis/trunk/atlantis/atecology/atq10.c

Fixed a missing break

Atlantis model used: Atlantis Model for Puget Sound https://github.com/hmorzaria/psatlantismodel commit 87031b7

Atlantis revision comments

Version 6717

Date pulled: June 24, 2024

OS: Ubuntu 20.04 LTS

Environment: Linux

Modeler: Hem Nalini Morzaria-Luna

Notes

Model behavior

Model behavior for functional groups was back to before 6716 when there was a missing break in the modified atq10.c corrected in this version

`case base_q10_id: /* Basic q10 relationship */
 ans = (double)pow(FunctGroupArray[sp].speciesParams[q10_id], (*current_corr));
 case humped_griffith_q10_id: /* Humped shape from Hary Griffith */`

Code changes

Versions compared 6717 6716 FILE COMPARED atassess/atassess_2013.vcxproj.bec

FILE COMPARED atassess/atassessParamIO.c

FILE COMPARED atassess/atAssessTierSetup.c

FILE COMPARED atassess/atattribute.c

FILE COMPARED atassess/atclassical.c

FILE COMPARED atassess/atdatareading.c

FILE COMPARED atassess/atdiet.c

FILE COMPARED atassess/atindices.c

FILE COMPARED atassess/atnetwork.c

FILE COMPARED atassess/atsample.c

FILE COMPARED atassess/atsamplesetup.c

FILE COMPARED atassess/atsolve.c

FILE COMPARED atassess/atsurvey.c

FILE COMPARED atassess/atwriting.c

FILE COMPARED atassess/doolittle.c

FILE COMPARED atassess/unit_lower_triangular.c

FILE COMPARED atassess/upper_triangular.c

FILE COMPARED atbrokerlink/atBrokerLinkInit.c

FILE COMPARED atbrokerlink/Deserialiser.c

FILE COMPARED atbrokerlink/ImportExportData.c

FILE COMPARED atbrokerlink/LinkageInterface.c

FILE COMPARED atbrokerlink/network.c

FILE COMPARED atbrokerlink/NetworkError.c

FILE COMPARED atbrokerlink/requests.pb-c.c

FILE COMPARED atbrokerlink/responses.pb-c.c

FILE COMPARED atCLAMLink/atCLAMComm.c

FILE COMPARED atCLAMLink/atCLAMImplement.c

FILE COMPARED atCLAMLink/atCLAMLink.c

FILE COMPARED atCLAMLink/atCLAMLinkIO.c

FILE COMPARED atCLAMLink/atCLAMLinkSetup.c

FILE COMPARED atCLAMLink/atCLAMManage.c

FILE COMPARED atecology/additionalTracer.c

FILE COMPARED atecology/atannualbiology.c

FILE COMPARED atecology/atbiolmessage.c

FILE COMPARED atecology/atbiology.c

FILE COMPARED atecology/atBiologyXMLParamIO.c

FILE COMPARED atecology/atbiolsetup.c

FILE COMPARED atecology/atbiolUtil.c

FILE COMPARED atecology/atbiophysics.c

FILE COMPARED atecology/atBuildTracer.c

FILE COMPARED atecology/atcalibtools.c

FILE COMPARED atecology/atContaminants.c

FILE COMPARED atecology/atcoral.c

FILE COMPARED atecology/atdemography.c

FILE COMPARED atecology/atdiversity.c

FILE COMPARED atecology/atecology_2013.vcxproj.bec

FILE COMPARED atecology/atecology.c Apply_Q10_Corrections(bm); | Apply_Q10_Corrections(bm, llogfp); Apply_Q10_Corrections(bm); | Apply_Q10_Corrections(bm, llogfp); Apply_Q10_Corrections(bm); | Apply_Q10_Corrections(bm, llogfp);

FILE COMPARED atecology/atecologyts.c

FILE COMPARED atecology/atexternalpop.c

FILE COMPARED atecology/atExternalScalar.c

FILE COMPARED atecology/atfluxbreakdown.c

FILE COMPARED atecology/atForcedMovement.c

FILE COMPARED atecology/atGroupProcesses.c

FILE COMPARED atecology/atIceProcesses.c FunctGroupArray[sp].Tcorr = Get_Tcorr | FunctGroupArray[sp].Tcorr = Get_Tcorr

FILE COMPARED atecology/atImposeRecruit.c

FILE COMPARED atecology/atLandProcess.c

FILE COMPARED atecology/atmacrophytes.c

FILE COMPARED atecology/atmigration.c if (check_day > (MIGRATION[species].Return_Now[co | if (check_day > (MIGRATION[species].Return_Now[co

FILE COMPARED atecology/atmovement.c

FILE COMPARED atecology/atNutrient.c

FILE COMPARED atecology/atPhysChemIO.c

FILE COMPARED atecology/atprocess.c

FILE COMPARED atecology/atq10.c > fprintf(“Scale linear mortality species = %d, cohort = %d >
>
> fprintf(”Scaler for linear mortality species = %d, cohort >
> fprintf(“Scaled linear mort species = %d, cohort = %d, sc >
} else | fprintf(llogfp,”Q10 flag activated, Time: %e, Tcorr >
> } else { | fprintf(llogfp,“Q10 flag not active, Time: %e, Tcor >
> } //Bad fprint leads to segmentation fault | > /* led to segmentation fault in 6704 FunctGroupArray[sp].Tcorr = Get_Tcorr(bm, sp, | FunctGroupArray[sp].Tcorr = Get_Tcorr(bm, sp, FunctGroupArray[sp].TcorrEff = FunctGroupArray[sp].Tc | FunctGroupArray[sp].TcorrEff = FunctGroupArray[sp].Tcorr; |
> fprintf(llogfp,”Calculating ParameterQ10, Time: %e, %s, >
Apply_Q10_Corrections(bm); | Apply_Q10_Corrections(bm, llogfp); double Get_Tcorr(MSEBoxModel bm, int sp, double current_temp | double Get_Tcorr(MSEBoxModel bm, int sp, double current_temp >
> fprintf(llogfp, “Q10 flag activated, going into Tco >
> fprintf(bm->logFile,”Base is activated Q10 - T >
>
> fprintf(llogfp, “Griffith activated Time: %e, /* | fprintf(bm->logFile,”Heinichen is activated if(sp == 45) { |
> /* if(sp == 45) { } | } / / |
|
> fprintf(bm->logFile, “CEATTLE is activated Ti >
void Apply_Q10_Corrections(MSEBoxModel bm) { | void Apply_Q10_Corrections(MSEBoxModel bm, FILE *llogfp) { double TscalarEff = 1.0; | double TscalarEff = 1.0; > fprintf(llogfp, “pHCorr value Time: %e, pHCorr = %e”, b >
>
> fprintf(llogfp, “Species is pH sens >
|
> fprintf(llogfp,”Invertebrate growth parameters Time: >
> fprintf(llogfp, “growth_scalar Time: >
| fprintf(”sp = %d, cohort = %d, Tcorr correction ove >
> fprintf(llogfp, “Vertebrate p >
> fprintf(llogfp,”Tscalar Time: %e, species = >
| fprintf(“sp = %d, Tcorr correction over vertebrate growth Fun > fprintf(llogfp,”Physical parameters Time: %e, r_DL = %e, r_D >
>

FILE COMPARED atecology/attime.c

FILE COMPARED atecology/atvertprocesses.c

FILE COMPARED atecology/dump.c

FILE COMPARED atecology/init.c

FILE COMPARED ateconomic/ateconeffort.c

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FILE COMPARED ateconomic/ateconomic_2013.vcxproj.bec

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FILE COMPARED ateconomic/atEconomicAnnual.c

FILE COMPARED ateconomic/ateconomicsetup.c

FILE COMPARED ateconomic/atEconomicUtil.c

FILE COMPARED ateconomic/ateconParamIO.c

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FILE COMPARED ateconomic/ateffortquota.c

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FILE COMPARED atharvest/atHarvestDiscards.c

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FILE COMPARED atharvest/atHarvestIO.c

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FILE COMPARED atharvest/atHarvestSetup.c

FILE COMPARED atharvest/atHarvestTS.c

FILE COMPARED atimplementation/atimplementation_2013.vcxproj.bec

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FILE COMPARED atlantisUtil/atlantisUtil_2013.vcxproj.bec

FILE COMPARED atlantisUtil/atUtil.c

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FILE COMPARED atlantisUtil/atUtilFisheryIO.c

FILE COMPARED atlantisUtil/atUtilFisheryXML.c

FILE COMPARED atlantisUtil/atUtilGroupIO.c

FILE COMPARED atlantisUtil/atUtilhelp.c

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FILE COMPARED atlantisUtil/atUtilUnix.c

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FILE COMPARED atlink/atComms.c

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FILE COMPARED atmanage/atmanage_2013.vcxproj.bec

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FILE COMPARED atmanage/atManageIndex.c

FILE COMPARED atmanage/atManageIO.c

FILE COMPARED atmanage/atManageMPATS.c

FILE COMPARED atmanage/atManageParamIO.c

FILE COMPARED atmanage/atManageSetup.c

FILE COMPARED atmanage/atManageTier.c

FILE COMPARED atmanage/atPGMSY.c

FILE COMPARED atmanage/atRlink.c

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FILE COMPARED atmanage/atRlinkRBC.c

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FILE COMPARED atmanage/atSS3assess.c

FILE COMPARED atphysics/atagetracerIO.c

FILE COMPARED atphysics/atbioirrig.c

FILE COMPARED atphysics/atbioturb.c

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FILE COMPARED atphysics/atdiagIO.c

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FILE COMPARED atphysics/atfishstatIO.c

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FILE COMPARED ConvertAtlantis/atAssesstoXML.c

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